|
| Status |
Public on Dec 19, 2018 |
| Title |
spleen_koxpbs_bs029 |
| Sample type |
SRA |
| |
|
| Source name |
lincRNA-Cox2 knockout Spleen PBS
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
genotype: lincRNA-Cox2 knockout
treatment: PBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following in vivo LPS challenge in which mice were injected by the intraperitoneal route with 20mg/kg LPS intraperitoneal lungs and spleens were extracted and placed in Trizol. RNA was extracted and 3ug was used to prepare libraries using illumna mRNA isolation kits
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
29_Spleen_KO_P
|
| Data processing |
RNAseq 1: the 150x150bp pairedEnd reads were trimmed by 50bp at the 3prime end to 100x100bp
RNAseq 2: reads mapping (by bowtie2) to mouse repeatMasker elements were discarded
RNAseq 3: reads were mapped to mm10 by STAR (2.5.3a), aided by a gtf file based on Gencode VM9basic with 100bp overlap
RNAseq 4: duplicate read mappings of the same start and end position were discarded using samtools rmdup.
RNAseq 5: bam files were converted to mm10 genomic coverage using bedtools genomeCoverageBed
RNAseq 6: the dup-removed coverage was used to extract coverage of all exonic positions for each gene in UCSC KnownGenes for mm10.
RNAseq 7: the exonic coverage (from paired-end 100x100bp reads) for each gene was divided by 200 to get read counts per gene for input to DESeq2
RNAseq 8: DESeq2 was run using the read counts for UCSC KnownGenes.
RNAseq 9: DESeq2 pairwise comparisons were separately performed for lung tissue samples and spleen tissue samples.
RNAseq 10: Within each tissue, wild-type samples were compared to mutant and knockout samples. Mutant and knockout samples were compared to each other.
Genome_build: mm10
Supplementary_files_format_and_content: There are two text files containing all differentially expressed genes following LPS stimulation in the lung and spleen as measured using DESeq2 analysis. There is one Excel file with a separate worksheet for each DESeq2 pairwise comparison for some subset of genes that displayed a log2fold change of 1.2 with a P value of less than 0.05
|
| |
|
| Submission date |
Jun 27, 2018 |
| Last update date |
Dec 19, 2018 |
| Contact name |
Susan Carpenter |
| E-mail(s) |
sucarpen@ucsc.edu
|
| Phone |
8315028155
|
| Organization name |
University of California Santa Cruz
|
| Department |
Molecular Cell and Developmental Biology
|
| Lab |
Carpenter Lab
|
| Street address |
1156 High Street
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE116354 |
Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (lungs and spleens) |
| GSE117379 |
Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo |
|
| Relations |
| BioSample |
SAMN09502908 |
| SRA |
SRX4314370 |
